create inositol molecule

From: politr_at_huji.ac.il
Date: Wed Dec 03 2008 - 10:48:38 CST

Dear NAMD users and developers,
I'm trying to build inositol molecule with psfgen. The problem is that I
don't have a topology definitions for this molecule so I tried to use
the existing definitions for some cyclic carbohydrate molecules. I'm
getting a cyclic molecule (chair conformation) but on some carbons I get
a strange angles for OH. In addition, when I try to change this angles I
get nothing. I have already read the information about the structure of
topology file and parameters that specified in the topology file but I
still can't build the proper structure of needed stereoisomer. I would
appreciate it very much if someone could help me with this problem. In
addition I would like to know if I can use the existing definitions for
some carbohydrate molecule (4C1 alpha-D-glucopyranose monomer) in order
to build inositol.
Thank you very much.

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